Vanillin production

In 2010, Brochado et al used heuristic optimization together with flux simulations to design a vanillin producing yeast strain.

Brochado, A. R., Andrejev, S., Maranas, C. D., & Patil, K. R. (2012). Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks. PLoS Computational Biology, 8(11), e1002758. doi:10.1371/journal.pcbi.1002758

Genome-scale metabolic model

In their work, the authors used iFF708 model, but recent insights in Yeast yielded newer and more complete versions. The latest version of S. cerevisiae model is Yeast 7.6. This model constains a higher coverage of gene functions.

Becuase this algorithms should be agnostic to the model, we implement the same strategy with the latest model.

from cameo import models

model = models.minho.yeast_7_6

#Fix gene rules compatibility
for reaction in model.reactions:
    while "AND" in reaction.gene_reaction_rule or "OR" in reaction.gene_reaction_rule:
        reaction.gene_reaction_rule = reaction._gene_reaction_rule.replace("AND", "and").replace("OR", "or")

cobra/io/sbml.py:149 UserWarning: charge of s_0330 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0332 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0334 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0337 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0338 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0339 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0404 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0428 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0429 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0430 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0431 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0432 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0433 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0450 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0535 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0536 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0537 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0542 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0574 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0620 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0628 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0709 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0710 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0713 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0747 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0748 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0749 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0757 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0773 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0774 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0811 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0812 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0832 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0833 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0847 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0848 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0891 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0892 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_0893 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1077 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1078 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1096 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1098 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1099 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1100 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1107 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1108 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1113 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1114 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1115 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1148 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1149 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1314 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1315 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1379 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1410 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1428 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1491 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1492 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1527 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1528 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1533 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1534 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1561 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1562 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1582 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1583 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1584 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1585 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1586 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1587 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1588 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1589 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1590 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1591 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1592 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1593 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1594 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1595 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1596 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1597 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1598 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1599 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1600 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1601 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1602 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1603 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1604 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1605 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1606 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1607 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1608 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1609 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1610 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1611 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1612 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1613 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1614 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1615 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1616 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1617 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1618 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1619 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1620 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1621 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1622 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1623 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_1845 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2770 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2771 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2772 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2773 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2774 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2775 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2776 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2777 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2778 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2779 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2780 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2793 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2795 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2810 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2812 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2813 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2814 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2822 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2824 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2828 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2829 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2858 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2861 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2862 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2863 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2868 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2871 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2872 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2878 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2879 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2880 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2881 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2882 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2883 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2884 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2885 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2886 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2887 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2888 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2889 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2890 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2891 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2892 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2893 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2894 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2895 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2896 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2897 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2898 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2899 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2900 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2901 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2902 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2903 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2904 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2905 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2906 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2907 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2908 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2909 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2910 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2911 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2912 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2913 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2915 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2916 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2920 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2921 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2922 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2923 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2924 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2925 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2926 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2927 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2928 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2929 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2930 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2931 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2932 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2933 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2935 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2936 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2937 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2938 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2940 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2941 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2942 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2943 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2944 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2945 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2946 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2947 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2948 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2949 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2950 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2951 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2954 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2955 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2956 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2957 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2958 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2959 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2960 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2961 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2962 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2963 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2964 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2965 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2967 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2968 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2969 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2970 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2971 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2972 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2973 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2974 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2975 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2978 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2979 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2980 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2981 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2982 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2983 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2984 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2985 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2986 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2987 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2988 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2989 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2990 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2991 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2992 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2993 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2996 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2997 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2998 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_2999 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3000 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3001 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3002 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3003 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3004 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3005 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3006 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3007 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3008 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3009 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3010 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3011 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3012 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3013 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3014 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3015 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3016 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3017 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3018 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3019 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3020 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3021 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3022 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3023 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3024 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3025 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3026 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3027 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3028 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3029 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3030 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3031 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3032 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3033 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3034 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3035 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3036 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3037 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3038 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3039 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3040 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3041 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3042 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3043 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3044 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3045 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3046 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3047 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3048 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3049 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3050 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3051 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3052 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3053 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3054 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3055 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3056 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3057 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3058 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3059 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3060 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3061 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3062 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3063 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3064 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3065 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3066 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3067 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3068 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3069 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3070 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3071 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3072 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3073 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3074 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3075 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3076 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3077 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3078 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3079 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3080 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3081 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3082 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3084 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3085 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3086 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3087 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3088 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3089 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3090 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3091 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3092 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3096 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3097 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3098 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3099 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3100 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3101 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3102 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3103 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3104 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3105 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3106 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3109 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3110 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3111 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3112 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3113 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3114 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3115 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3116 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3118 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3119 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3120 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3121 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3122 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3123 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3124 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3125 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3126 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3127 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3128 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3130 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3131 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3132 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3133 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3134 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3135 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3136 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3137 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3138 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3139 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3140 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3141 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3142 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3143 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3144 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3145 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3148 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3149 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3150 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3151 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3152 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3153 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3154 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3155 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3156 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3157 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3158 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3159 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3160 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3161 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3162 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3163 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3166 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3167 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3168 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3169 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3170 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3171 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3172 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3173 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3174 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3175 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3176 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3177 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3178 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3179 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3180 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3181 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3184 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3185 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3186 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3187 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3188 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3189 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3190 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3191 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3192 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3193 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3194 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3195 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3196 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3197 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3198 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3199 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3200 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3201 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3202 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3203 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3204 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3205 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3206 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3207 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3208 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3209 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3210 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3211 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3212 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3213 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3214 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3220 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3221 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3222 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3223 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3224 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3225 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3227 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3229 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3230 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3231 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3232 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3233 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3234 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3235 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3236 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3237 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3238 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3239 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3240 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3241 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3242 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3243 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3244 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3245 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3246 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3247 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3248 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3249 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3250 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3251 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3252 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3253 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3254 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3255 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3256 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3257 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3258 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3259 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3260 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3261 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3262 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3263 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3264 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3265 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3266 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3267 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3268 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3269 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3270 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3272 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3273 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3274 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3275 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3276 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3278 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3279 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3280 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3281 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3282 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3283 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3284 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3285 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3286 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3287 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3288 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3289 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3290 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3291 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3292 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3293 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3294 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3295 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3296 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3297 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3298 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3299 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3300 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3301 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3302 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3303 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3304 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3305 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3306 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3307 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3308 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3309 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3310 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3311 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3312 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3313 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3314 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3315 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3316 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3317 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3318 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3319 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3323 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3325 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3326 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3327 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3328 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3329 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3330 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3331 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3332 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3333 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3334 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3335 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3336 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3337 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3338 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3339 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3340 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3343 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3344 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3345 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3346 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3347 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3348 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3349 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3350 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3351 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3352 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3353 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3354 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3355 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3356 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3357 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3358 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3361 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3362 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3363 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3364 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3365 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3366 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3367 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3368 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3369 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3370 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3371 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3372 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3373 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3374 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3375 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3376 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3377 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3378 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3379 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3380 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3381 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3382 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3383 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3384 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3385 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3386 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3387 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3388 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3389 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3390 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3391 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3392 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3393 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3394 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3395 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3396 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3397 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3398 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3399 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3400 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3401 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3402 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3403 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3404 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3405 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3406 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3407 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3408 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3409 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3410 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3411 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3412 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3413 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3414 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3415 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3416 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3417 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3418 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3419 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3420 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3421 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3422 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3423 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3424 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3425 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3426 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3427 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3428 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3429 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3430 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3431 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3448 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3450 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3452 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3453 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3454 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3455 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3456 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3457 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3458 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3460 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3461 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3462 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3465 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3466 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3467 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3468 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3469 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3470 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3471 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3472 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3473 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3474 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3475 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3476 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3477 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3478 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3479 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3480 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3481 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3482 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3483 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3484 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3485 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3486 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3487 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3488 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3489 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3490 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3491 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3492 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3493 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3494 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3496 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3497 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3499 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3500 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3501 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3502 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3503 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3504 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3505 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3506 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3507 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3508 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3509 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3510 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3511 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3512 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3513 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3514 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3515 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3516 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3517 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3518 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3519 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3520 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3521 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3522 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3523 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3524 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3525 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3526 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3527 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3528 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3529 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3530 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3531 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3532 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3533 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3534 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3535 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3537 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3538 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3539 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3540 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3541 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3542 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3543 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3544 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3545 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3546 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3547 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3548 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3549 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3550 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3551 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3552 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3553 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3554 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3555 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3556 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3557 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3558 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3559 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3560 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3561 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3562 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3563 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3564 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3565 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3566 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3567 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3568 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3569 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3570 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3571 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3572 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3573 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3574 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3575 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3576 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3577 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3578 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3579 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3580 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3581 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3582 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3583 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3584 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3585 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3586 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3587 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3588 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3589 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3590 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3591 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3592 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3593 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3594 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3595 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3596 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3597 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3598 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3599 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3600 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3601 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3602 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3603 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3604 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3605 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3606 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3607 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3608 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3609 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3610 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3611 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3612 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3613 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3614 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3615 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3616 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3617 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3618 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3619 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3620 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3621 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3622 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3623 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3624 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3625 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3626 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3627 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3628 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3629 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3630 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3631 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3632 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3633 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3634 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3635 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3636 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3637 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3638 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3639 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3640 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3641 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3642 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3643 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3644 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3645 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3646 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3647 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3648 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3649 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3650 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3651 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3652 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3653 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3654 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3655 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3671 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3672 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3673 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3674 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3675 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3676 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3678 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3679 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3680 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3681 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3682 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3683 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3685 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3686 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3687 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3688 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3689 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3690 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3691 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3692 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3693 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3694 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3695 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3696 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3697 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3698 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3699 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3700 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3701 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3702 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3703 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3704 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3705 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3706 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3707 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3708 is not a number ()
cobra/io/sbml.py:149 UserWarning: charge of s_3714 is not a number ()
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YDL174C AND YEL039C) OR (YDL174C AND YJR048W) OR (YEL039C AND YEL071W) OR (YEL071W AND YJR048W))' for <Reaction r_0001 at 0x111a0a0f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YDL178W AND YEL039C) OR (YDL178W AND YJR048W))' for <Reaction r_0002 at 0x111a0a390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YEL039C AND YML054C) OR (YJR048W AND YML054C))' for <Reaction r_0004 at 0x111a0a630>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR032W OR YLR342W)' for <Reaction r_0005 at 0x111a0a828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR143W OR YPR159W)' for <Reaction r_0006 at 0x111a0a978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL038W AND YMR009W)' for <Reaction r_0013 at 0x111a0acc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YCL009C AND YMR108W) OR YMR108W)' for <Reaction r_0016 at 0x111a25080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER152C OR YGL202W OR YJL060W)' for <Reaction r_0018 at 0x111a252e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR204W AND YGL119W AND YGR255C AND YLR201C AND YML110C AND YOL096C AND YOR125C)' for <Reaction r_0021 at 0x111a256d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR204W AND YGL119W AND YGR255C AND YLR201C AND YML110C AND YOL096C AND YOR125C)' for <Reaction r_0022 at 0x111a25a90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL104C OR YOR108W)' for <Reaction r_0024 at 0x111a25ef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL248W OR YOR360C)' for <Reaction r_0033 at 0x111a2c780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR249C OR YDR035W)' for <Reaction r_0042 at 0x111a300f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR087C OR YLR044C OR YLR134W)' for <Reaction r_0062 at 0x111a30978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL080C OR YGR087C OR YLR044C OR YLR134W)' for <Reaction r_0064 at 0x111a30c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR410W OR YOR163W)' for <Reaction r_0073 at 0x111a36588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER037W OR YGL224C)' for <Reaction r_0076 at 0x111a36908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER037W OR YGL224C)' for <Reaction r_0078 at 0x111a36b70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL125W OR YPL023C)' for <Reaction r_0080 at 0x111a36dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL107C OR YOL136C)' for <Reaction r_0090 at 0x111a3c780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR248W OR YHR163W)' for <Reaction r_0091 at 0x111a3c908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR410W OR YOR163W)' for <Reaction r_0092 at 0x111a3ca58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR087C OR YLR044C OR YLR134W)' for <Reaction r_0095 at 0x111a3ccc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YCL009C AND YMR108W) OR YMR108W)' for <Reaction r_0097 at 0x111a3cf98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL141W AND YNR016C)' for <Reaction r_0109 at 0x111a44ac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL054C OR YLR153C)' for <Reaction r_0112 at 0x111a44d30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAR071W OR YBR093C)' for <Reaction r_0116 at 0x111a4c208>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W)' for <Reaction r_0127 at 0x111a4cd30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W)' for <Reaction r_0132 at 0x111a53240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR177C OR YOR377W)' for <Reaction r_0158 at 0x111a59ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR177C OR YOR377W)' for <Reaction r_0159 at 0x111a59d30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR177C OR YOR377W)' for <Reaction r_0160 at 0x111a59e80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR177C OR YOR377W)' for <Reaction r_0161 at 0x111a59fd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR177C OR YOR377W)' for <Reaction r_0162 at 0x111a5f160>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR368W OR YHR104W)' for <Reaction r_0164 at 0x111a5f390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL256W OR YMR083W)' for <Reaction r_0165 at 0x111a5f518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR145W OR YDL168W OR YOL086C)' for <Reaction r_0166 at 0x111a5f668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL256W OR YMR083W)' for <Reaction r_0167 at 0x111a5f828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR105W OR YDR368W OR YMR318C)' for <Reaction r_0168 at 0x111a5f978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR145W OR YDL168W OR YOL086C)' for <Reaction r_0169 at 0x111a5fb38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL256W OR YMR083W)' for <Reaction r_0170 at 0x111a5fcf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR105W OR YMR318C)' for <Reaction r_0171 at 0x111a5fe48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR169C OR YMR170C)' for <Reaction r_0172 at 0x111a5ff98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER073W OR YOR374W)' for <Reaction r_0175 at 0x111a65320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER073W OR YOR374W)' for <Reaction r_0178 at 0x111a65630>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR145W OR YDL168W OR YOL086C)' for <Reaction r_0179 at 0x111a657b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL256W OR YMR083W)' for <Reaction r_0180 at 0x111a65978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR105W OR YMR318C)' for <Reaction r_0181 at 0x111a65ac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR145W OR YDL168W OR YOL086C)' for <Reaction r_0182 at 0x111a65c18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL256W OR YMR083W)' for <Reaction r_0183 at 0x111a65dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR105W OR YMR318C)' for <Reaction r_0184 at 0x111a65f28>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR169C OR YMR170C)' for <Reaction r_0185 at 0x111a6c0b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR145W OR YDL168W OR YOL086C)' for <Reaction r_0186 at 0x111a6c208>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGL256W OR YMR083W)' for <Reaction r_0187 at 0x111a6c3c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR199W OR YBR205W OR YDR483W OR YJL139C OR YKR061W OR YNL029C OR YOR099W OR YPL053C)' for <Reaction r_0192 at 0x111a6c940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR126C AND YDR074W AND YML100W) OR (YBR126C AND YDR074W AND YMR261C))' for <Reaction r_0195 at 0x111a6cf60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR299W OR YGR287C OR YGR292W OR YIL172C OR YJL216C OR YJL221C)' for <Reaction r_0198 at 0x111a71208>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER090W AND YKL211C)' for <Reaction r_0203 at 0x111a71898>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR124W OR YPR145W)' for <Reaction r_0211 at 0x111a761d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((Q0080 AND Q0085 AND Q0130 AND YBL099W AND YBR039W AND YDL004W AND YDR298C AND YDR322C-A AND YDR377W AND YJR121W AND YKL016C AND YLR295C AND YML081C-A AND YPL078C AND YPL271W) OR (Q0080 AND Q0085 AND Q0130 AND YBL099W AND YBR039W AND YDL004W AND YDR298C AND YDR377W AND YJR121W AND YKL016C AND YLR295C AND YML081C-A AND YPL078C AND YPL271W AND YPR020W))' for <Reaction r_0226 at 0x111a7d240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YCR024C-A AND YEL017C-A AND YGL008C) OR (YCR024C-A AND YEL017C-A AND YPL036W) OR YER005W)' for <Reaction r_0227 at 0x111a7d978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL090C AND YKL019W)' for <Reaction r_0249 at 0x111a84c18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL130C OR (YJR109C AND YOR303W))' for <Reaction r_0250 at 0x111a84da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAR035W OR YER024W)' for <Reaction r_0252 at 0x111a84f60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YHL003C AND YMR298W) OR (YKL008C AND YMR298W))' for <Reaction r_0263 at 0x111a8b8d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YHL003C AND YMR298W) OR (YKL008C AND YMR298W))' for <Reaction r_0264 at 0x111a8bac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YHL003C AND YMR298W) OR (YKL008C AND YMR298W))' for <Reaction r_0265 at 0x111a8bc88>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YHL003C AND YMR298W) OR (YKL008C AND YMR298W))' for <Reaction r_0266 at 0x111a8be48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR307W OR YLR308W)' for <Reaction r_0271 at 0x111a91390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR023C OR YBR038W OR YNL192W)' for <Reaction r_0272 at 0x111a91518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0281 at 0x111a91c18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0282 at 0x111a91da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0283 at 0x111a91ef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0284 at 0x111a99080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0285 at 0x111a991d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0286 at 0x111a99320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0287 at 0x111a99470>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0288 at 0x111a995c0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0289 at 0x111a99710>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0290 at 0x111a99860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0291 at 0x111a999b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0292 at 0x111a99b00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0293 at 0x111a99c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0294 at 0x111a99da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0295 at 0x111a99ef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0296 at 0x111aa0080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0297 at 0x111aa01d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0298 at 0x111aa0320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR002C OR YMR101C)' for <Reaction r_0299 at 0x111aa0470>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNR001C OR YPR001W)' for <Reaction r_0300 at 0x111aa05c0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL039C OR YJR103W)' for <Reaction r_0306 at 0x111aa0ac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL039C OR YJR103W)' for <Reaction r_0307 at 0x111aa0c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR007C AND YHR042W)' for <Reaction r_0317 at 0x111aa6668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFL053W OR YML070W)' for <Reaction r_0354 at 0x111ab1588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YAL023C AND YDL095W) OR YDL093W OR YJR143C OR YOR321W)' for <Reaction r_0362 at 0x111ab1e10>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR254W OR YHR174W)' for <Reaction r_0366 at 0x111ab5438>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR147W OR YLR133W)' for <Reaction r_0368 at 0x111ab55f8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR261C OR YGR282C OR YLR300W OR YNR067C OR YOR190W)' for <Reaction r_0370 at 0x111ab5828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YEL039C AND YKR066C) OR (YJR048W AND YKR066C))' for <Reaction r_0437 at 0x111ab91d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((Q0045 AND Q0250 AND Q0275 AND YDL067C AND YEL039C AND YGL187C AND YGL191W AND YHR051W AND YIL111W AND YLR038C AND YLR395C AND YMR256C) OR (Q0045 AND Q0250 AND Q0275 AND YDL067C AND YEL039C AND YGL187C AND YGL191W AND YHR051W AND YLR038C AND YLR395C AND YMR256C AND YNL052W) OR (Q0045 AND Q0250 AND Q0275 AND YDL067C AND YGL187C AND YGL191W AND YHR051W AND YIL111W AND YJR048W AND YLR038C AND YLR395C AND YMR256C) OR (Q0045 AND Q0250 AND Q0275 AND YDL067C AND YGL187C AND YGL191W AND YHR051W AND YJR048W AND YLR038C AND YLR395C AND YMR256C AND YNL052W))' for <Reaction r_0438 at 0x111ab93c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((Q0105 AND YBL045C AND YDR529C AND YEL024W AND YEL039C AND YFR033C AND YGR183C AND YHR001W-A AND YJL166W AND YOR065W AND YPR191W) OR (Q0105 AND YBL045C AND YDR529C AND YEL024W AND YFR033C AND YGR183C AND YHR001W-A AND YJL166W AND YJR048W AND YOR065W AND YPR191W))' for <Reaction r_0439 at 0x111ab9a20>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL062W OR YOR375C)' for <Reaction r_0471 at 0x111ac6d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YCL035C AND YPL091W) OR (YDR098C AND YPL091W) OR (YDR513W AND YPL091W) OR (YER174C AND YPL091W))' for <Reaction r_0481 at 0x111acb710>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YPL059W AND YPL091W)' for <Reaction r_0482 at 0x111acb9e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR244W OR YCL035C OR YDR513W OR YIR037W OR YKL026C)' for <Reaction r_0483 at 0x111acbb38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR192C OR YJL052W OR YJR009C)' for <Reaction r_0486 at 0x111acbfd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER062C OR YIL053W)' for <Reaction r_0489 at 0x111ad3400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL022W OR YOL059W)' for <Reaction r_0491 at 0x111ad3668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_0501 at 0x111ad3b70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_0504 at 0x111ad3fd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YAL044C AND YDR019C AND YFL018C AND YMR189W) OR (YDR148C AND YFL018C AND YIL125W))' for <Reaction r_0505 at 0x111ada278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_0506 at 0x111ada588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_0507 at 0x111ada7b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_0508 at 0x111ada9e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_0509 at 0x111adac18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YFR015C AND YJL137C) OR (YFR015C AND YKR058W) OR (YJL137C AND YLR258W) OR (YKR058W AND YLR258W))' for <Reaction r_0510 at 0x111adae48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR121C OR YPR081C)' for <Reaction r_0512 at 0x111ae0198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL052C AND YJR013W)' for <Reaction r_0519 at 0x111ae0518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR302W OR YLL031C)' for <Reaction r_0523 at 0x111ae09b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR376W AND YPL252C)' for <Reaction r_0530 at 0x111ae5160>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR204W AND YGL119W AND YGR255C AND YLR201C AND YML110C AND YOL096C AND YOR125C)' for <Reaction r_0532 at 0x111ae53c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFR053C OR YGL253W)' for <Reaction r_0533 at 0x111ae5780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL040W OR YFR053C OR YGL253W)' for <Reaction r_0534 at 0x111ae58d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFR053C OR YGL253W)' for <Reaction r_0535 at 0x111ae5a90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL131W OR YDL182W)' for <Reaction r_0543 at 0x111aec320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLL062C OR YPL273W)' for <Reaction r_0544 at 0x111aec4a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YDR453C AND YGR209C) OR (YDR453C AND YLR043C))' for <Reaction r_0550 at 0x111aecb00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL064C AND YCR083W)' for <Reaction r_0551 at 0x111aeccf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YGR209C AND YLR109W) OR (YLR043C AND YLR109W))' for <Reaction r_0552 at 0x111aece48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR450W OR YML075C)' for <Reaction r_0558 at 0x111af2588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YOL055C OR YPL258C OR YPR121W)' for <Reaction r_0561 at 0x111af28d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR216W OR YLR432W OR YML056C)' for <Reaction r_0565 at 0x111af2da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR087C OR YLR044C OR YLR134W)' for <Reaction r_0567 at 0x111af70b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR028C OR YMR120C)' for <Reaction r_0570 at 0x111af74a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL037C AND YOR136W)' for <Reaction r_0658 at 0x111b11240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR244C AND YOR142W)' for <Reaction r_0668 at 0x111b11be0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR115C AND YGL154C)' for <Reaction r_0678 at 0x111b16550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR155C OR YLR157C OR YLR158C OR YLR160C)' for <Reaction r_0680 at 0x111b167b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR104W OR YOL151W)' for <Reaction r_0688 at 0x111b16da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIR031C OR YNL117W)' for <Reaction r_0716 at 0x111b237f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL192C AND YOR221C)' for <Reaction r_0721 at 0x111b23c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR502C OR YLR180W)' for <Reaction r_0726 at 0x111b281d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0747 at 0x111b2e048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0748 at 0x111b2e240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0749 at 0x111b2e400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0750 at 0x111b2e5c0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0751 at 0x111b2e780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0752 at 0x111b2e940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0753 at 0x111b2eb00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0754 at 0x111b2ecc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0755 at 0x111b2ee80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR036C AND YBR161W) OR (YBR036C AND YPL057C))' for <Reaction r_0756 at 0x111b35080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR287W OR YHR046C)' for <Reaction r_0757 at 0x111b35240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL071W OR YMR062C)' for <Reaction r_0761 at 0x111b35668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR402C AND YDR403W)' for <Reaction r_0763 at 0x111b358d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL041W OR YJR049C)' for <Reaction r_0765 at 0x111b35b38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL041W OR YJR049C OR YPL188W)' for <Reaction r_0766 at 0x111b35cc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL042C OR YDR191W OR YOL068C OR YOR025W OR YPL015C)' for <Reaction r_0767 at 0x111b35e80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL085W OR YMR145C)' for <Reaction r_0770 at 0x111b3d320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL041W OR YJR049C)' for <Reaction r_0771 at 0x111b3d4a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL041W OR YJR049C OR YPL188W)' for <Reaction r_0772 at 0x111b3d5f8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR010W OR YLR328W)' for <Reaction r_0784 at 0x111b3ddd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR010W OR YLR328W)' for <Reaction r_0785 at 0x111b3df60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YML106W OR YMR271C)' for <Reaction r_0820 at 0x111b49cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR148C AND YFL018C AND YIL125W)' for <Reaction r_0831 at 0x111b49f60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR148C AND YFL018C AND YIL125W)' for <Reaction r_0832 at 0x111b4f198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFL022C AND YLR060W)' for <Reaction r_0852 at 0x111b4fcf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YGR209C AND YPR167C) OR (YLR043C AND YPR167C))' for <Reaction r_0883 at 0x111b542e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR240C AND YMR205C)' for <Reaction r_0886 at 0x111b546d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR240C AND YMR205C)' for <Reaction r_0887 at 0x111b54860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL127W OR YMR105C)' for <Reaction r_0888 at 0x111b549b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR256W OR YHR183W)' for <Reaction r_0889 at 0x111b54b38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER081W OR YIL074C)' for <Reaction r_0891 at 0x111b549e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YOL055C OR YPL258C OR YPR121W)' for <Reaction r_0903 at 0x111b5c198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YKL088W AND YKR072C AND YOR054C) OR (YKL088W AND YKR072C) OR (YKL088W AND YOR054C) OR YKL088W)' for <Reaction r_0906 at 0x111b5c588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL127W OR YMR105C OR YMR278W)' for <Reaction r_0907 at 0x111b5c780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR028C OR YMR120C)' for <Reaction r_0912 at 0x111b5ccf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBL068W AND YOL061W) OR (YER099C AND YOL061W) OR (YHL011C AND YKL181W))' for <Reaction r_0916 at 0x111b60198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR400W AND YLR017W AND YLR209C)' for <Reaction r_0943 at 0x111b66438>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR218C OR YGL062W)' for <Reaction r_0958 at 0x111b66d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR087C OR YLR044C OR YLR134W)' for <Reaction r_0959 at 0x111b66ef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR087C OR YLR044C OR YLR134W)' for <Reaction r_0960 at 0x111b6c0f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR221C AND YER178W AND YFL018C AND YGR193C AND YNL071W)' for <Reaction r_0961 at 0x111b6c2b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL038W OR YOR347C)' for <Reaction r_0962 at 0x111b6c550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR204W AND YGL119W AND YGR255C AND YLR201C AND YML110C AND YOL096C AND YOR125C)' for <Reaction r_0963 at 0x111b6c6a0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER070W OR YGR180C OR YIL066C OR YJL026W)' for <Reaction r_0974 at 0x111b722e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER070W OR YGR180C OR YIL066C OR YJL026W)' for <Reaction r_0975 at 0x111b72550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER070W OR YGR180C OR YIL066C OR YJL026W)' for <Reaction r_0976 at 0x111b72780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER070W OR YGR180C OR YIL066C OR YJL026W)' for <Reaction r_0977 at 0x111b729b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER070W OR YGR180C OR YIL066C OR YJL026W)' for <Reaction r_0978 at 0x111b72be0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER070W OR YGR180C OR YIL066C OR YJL026W)' for <Reaction r_0979 at 0x111b72e10>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR204W AND YGL119W AND YGR255C AND YLR201C AND YML110C AND YOL096C AND YOR125C)' for <Reaction r_0985 at 0x111b7a390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR058C-A AND YDR062W AND YMR296C) OR (YDR062W AND YMR296C))' for <Reaction r_0993 at 0x111b7acc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR023W OR YHR011W)' for <Reaction r_0995 at 0x111b7ae80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL134W OR YKR053C)' for <Reaction r_1004 at 0x111b81780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL134W OR YKR053C)' for <Reaction r_1005 at 0x111b81908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR260W OR YOR171C)' for <Reaction r_1006 at 0x111b81a58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR260W OR YOR171C)' for <Reaction r_1007 at 0x111b81ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YDR178W AND YJL045W AND YKL141W AND YLL041C) OR (YDR178W AND YKL141W AND YKL148C AND YLL041C))' for <Reaction r_1021 at 0x111b860f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR244C AND YOR142W)' for <Reaction r_1022 at 0x111b863c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFR030W AND YJR137C)' for <Reaction r_1027 at 0x111b86908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YAL044C AND YDR019C AND YFL018C AND YMR189W)' for <Reaction r_1030 at 0x111b86b70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL132C OR YOR241W)' for <Reaction r_1031 at 0x111b86dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YGR209C AND YIL010W) OR (YIL010W AND YLR043C))' for <Reaction r_1037 at 0x111b8e400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YDR353W AND YGR209C) OR (YDR353W AND YLR043C) OR YDR353W)' for <Reaction r_1038 at 0x111b8e5f8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YCR083W AND YHR106W) OR (YCR083W AND YPL091W))' for <Reaction r_1039 at 0x111b8e7b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR117C OR YPR074C)' for <Reaction r_1049 at 0x111b93198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR117C OR YPR074C)' for <Reaction r_1050 at 0x111b93320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YBR126C AND YDR074W AND YML100W) OR (YBR126C AND YDR074W AND YMR261C))' for <Reaction r_1051 at 0x111b93470>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFL001W OR YGL063W OR YNL292W OR YPL212C)' for <Reaction r_1095 at 0x111b9e908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL131W OR YDL182W)' for <Reaction r_1838 at 0x111b9ec50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR145W OR YOL086C)' for <Reaction r_2115 at 0x111ba40f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL182W AND YPL231W)' for <Reaction r_2140 at 0x111ba4860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL182W AND YPL231W)' for <Reaction r_2141 at 0x111ba4a20>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER061C AND YKL192C)' for <Reaction r_2142 at 0x111ba4b70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER061C AND YKL192C)' for <Reaction r_2143 at 0x111ba4cc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER061C AND YKL192C)' for <Reaction r_2144 at 0x111ba4dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR034W OR YLR372W)' for <Reaction r_2157 at 0x111ba9ac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR034W OR YLR372W)' for <Reaction r_2158 at 0x111ba9c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR034W OR YLR372W)' for <Reaction r_2159 at 0x111ba9da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2195 at 0x111bb6668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2196 at 0x111bb67f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2197 at 0x111bb6940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2198 at 0x111bb6a90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2199 at 0x111bb6be0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2201 at 0x111bb6dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2202 at 0x111bb6f60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2203 at 0x111bbe0f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2204 at 0x111bbe240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR246W OR YOR317W)' for <Reaction r_2205 at 0x111bbe390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL011W OR YKR067W)' for <Reaction r_2308 at 0x111be0320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL011W OR YKR067W)' for <Reaction r_2309 at 0x111be04a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL011W OR YKR067W)' for <Reaction r_2312 at 0x111be07b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL011W OR YKR067W)' for <Reaction r_2313 at 0x111be0940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YOR175C)' for <Reaction r_2333 at 0x111be6ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YOR175C)' for <Reaction r_2335 at 0x111be6dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YOR175C)' for <Reaction r_2337 at 0x111bec048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YOR175C)' for <Reaction r_2339 at 0x111bec278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YKR089C OR YOR081C)' for <Reaction r_2340 at 0x111bec400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YKR089C OR YOR081C)' for <Reaction r_2341 at 0x111bec5c0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YKR089C OR YOR081C)' for <Reaction r_2342 at 0x111bec780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL052C OR YKR089C OR YOR081C)' for <Reaction r_2343 at 0x111bec978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2368 at 0x111bf80f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2369 at 0x111bf82e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2370 at 0x111bf84a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2371 at 0x111bf8668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2372 at 0x111bf8828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2373 at 0x111bf89e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2374 at 0x111bf8ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2375 at 0x111bf8d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2376 at 0x111bf8f28>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2377 at 0x111c00128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2378 at 0x111c002e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2379 at 0x111c004a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2380 at 0x111c00668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2381 at 0x111c00828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2382 at 0x111c009e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2383 at 0x111c00ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2384 at 0x111c00d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2385 at 0x111c00f28>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2386 at 0x111c07128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2387 at 0x111c072e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2388 at 0x111c074a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2389 at 0x111c07668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2390 at 0x111c07828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2391 at 0x111c079e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2392 at 0x111c07ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2393 at 0x111c07d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2394 at 0x111c07f28>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2395 at 0x111c0d128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2396 at 0x111c0d2e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2397 at 0x111c0d4a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2398 at 0x111c0d668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCR048W OR YNR019W OR YOR245C)' for <Reaction r_2399 at 0x111c0d828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2488 at 0x111c2f978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2489 at 0x111c2fb00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2490 at 0x111c2fc50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2491 at 0x111c2fda0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2492 at 0x111c2fef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2493 at 0x111c36080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2494 at 0x111c361d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR157W OR YJR073C)' for <Reaction r_2495 at 0x111c36320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2528 at 0x111c45160>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2529 at 0x111c45320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2530 at 0x111c45470>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2531 at 0x111c45438>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2532 at 0x111c456d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2533 at 0x111c45828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2534 at 0x111c45978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YHR123W OR YNL130C)' for <Reaction r_2535 at 0x111c45ac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2820 at 0x111cae278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2821 at 0x111cae438>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2822 at 0x111cae550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2823 at 0x111cae6a0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2824 at 0x111cae7f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2825 at 0x111cae940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2826 at 0x111caea90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJL100W OR YLR305C)' for <Reaction r_2827 at 0x111caebe0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2836 at 0x111cb6470>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2837 at 0x111cb65f8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2838 at 0x111cb6748>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2839 at 0x111cb6898>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2840 at 0x111cb69e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2841 at 0x111cb6b38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2842 at 0x111cb6c88>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR373W AND YNL267W)' for <Reaction r_2843 at 0x111cb6dd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2852 at 0x111cbb668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2853 at 0x111cbb7f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2854 at 0x111cbb940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2855 at 0x111cbba90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2856 at 0x111cbbbe0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2857 at 0x111cbbd30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2858 at 0x111cbbe80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR097W AND YLR240W)' for <Reaction r_2859 at 0x111cbbfd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3046 at 0x111cfde80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3047 at 0x111d05048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3048 at 0x111d05198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3049 at 0x111d052e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3050 at 0x111d05438>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3051 at 0x111d05588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3052 at 0x111d056d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3053 at 0x111d05828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3054 at 0x111d05978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3055 at 0x111d05ac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3056 at 0x111d05c18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YMR008C)' for <Reaction r_3057 at 0x111d05d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3058 at 0x111d05eb8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3059 at 0x111d0c048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3060 at 0x111d0c198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3061 at 0x111d0c2e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3062 at 0x111d0c438>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3063 at 0x111d0c588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3064 at 0x111d0c6d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3065 at 0x111d0c860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3066 at 0x111d0c9b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3067 at 0x111d0cb00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3068 at 0x111d0cc50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YMR006C OR YOL011W)' for <Reaction r_3069 at 0x111d0cd68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3112 at 0x111d1e4e0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3113 at 0x111d1e668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3114 at 0x111d1e7b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3115 at 0x111d1e908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3116 at 0x111d1ea58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3117 at 0x111d1eba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3118 at 0x111d1ecf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3119 at 0x111d1ee48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3120 at 0x111d1ef98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3121 at 0x111d26198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3122 at 0x111d26358>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3123 at 0x111d26518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3124 at 0x111d266d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3125 at 0x111d26898>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3126 at 0x111d26a58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YJR110W OR YNL106C OR YOR109W)' for <Reaction r_3127 at 0x111d26c18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3144 at 0x111d2ec18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3145 at 0x111d2eda0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3146 at 0x111d2eef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3147 at 0x111d35080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3148 at 0x111d351d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3149 at 0x111d35320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3150 at 0x111d35470>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3151 at 0x111d355c0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3152 at 0x111d35710>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3153 at 0x111d35860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3154 at 0x111d359b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3155 at 0x111d35b00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3156 at 0x111d35c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3157 at 0x111d35da0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3158 at 0x111d35ef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3159 at 0x111d3b080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3176 at 0x111d3bf98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3177 at 0x111d42160>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3178 at 0x111d422b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3179 at 0x111d42400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3180 at 0x111d42550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3181 at 0x111d426a0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3182 at 0x111d427f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3183 at 0x111d42940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3184 at 0x111d42a90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3185 at 0x111d42be0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3186 at 0x111d42d30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3187 at 0x111d42e80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3188 at 0x111d42fd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3189 at 0x111d4a160>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3190 at 0x111d4a2b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YNL106C OR YOR109W)' for <Reaction r_3191 at 0x111d4a400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3192 at 0x111d4a550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3193 at 0x111d4a710>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3194 at 0x111d4a8d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3195 at 0x111d4aa90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3196 at 0x111d4ac50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3197 at 0x111d4ae10>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3198 at 0x111d4afd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3199 at 0x111d511d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3200 at 0x111d51390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3201 at 0x111d51550>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3202 at 0x111d51710>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3203 at 0x111d518d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3204 at 0x111d51a90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3205 at 0x111d51c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3206 at 0x111d51e10>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL002C OR YNL106C OR YOR109W)' for <Reaction r_3207 at 0x111d51fd0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3216 at 0x111d588d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3217 at 0x111d58a58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3218 at 0x111d58ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3219 at 0x111d58cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3220 at 0x111d58e48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3221 at 0x111d58f98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3222 at 0x111d60128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR386W AND YNL325C)' for <Reaction r_3223 at 0x111d60278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL140W OR YLL012W)' for <Reaction r_3252 at 0x111d67c50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL140W OR YLL012W)' for <Reaction r_3253 at 0x111d67e10>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3264 at 0x111d6c860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3265 at 0x111d6cac8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3266 at 0x111d6ccf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3267 at 0x111d6cf28>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3268 at 0x111d6f198>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3269 at 0x111d6f3c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3270 at 0x111d6f5f8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3271 at 0x111d6f828>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3272 at 0x111d6fa58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3273 at 0x111d6fc88>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3274 at 0x111d6feb8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3275 at 0x111d76128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3276 at 0x111d76358>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3277 at 0x111d76588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3278 at 0x111d767b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3279 at 0x111d769e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3280 at 0x111d76c18>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3281 at 0x111d76e48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3282 at 0x111d7d0b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3283 at 0x111d7d2e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3284 at 0x111d7d518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3285 at 0x111d7d748>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3286 at 0x111d7d978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3287 at 0x111d7dba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3288 at 0x111d7ddd8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3289 at 0x111d84048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3290 at 0x111d84278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3291 at 0x111d844a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3292 at 0x111d846d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3293 at 0x111d84908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3294 at 0x111d84b38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR204C OR YKR089C OR YMR313C OR YOR081C)' for <Reaction r_3295 at 0x111d84d68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR127C AND YDL185W AND YEL027W AND YEL051W AND YGR020C AND YHR026W AND YHR039C-A AND YKL080W AND YLR447C AND YMR054W AND YOR332W AND YPL234C AND YPR036W)' for <Reaction r_1085 at 0x111d98588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR127C AND YDL185W AND YEL027W AND YEL051W AND YGR020C AND YHR026W AND YHR039C-A AND YKL080W AND YLR447C AND YOR270C AND YOR332W AND YPL234C AND YPR036W)' for <Reaction r_1086 at 0x111d98ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YOR222W OR YPL134C)' for <Reaction r_1099 at 0x111d9d2e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL210W OR YOR348C)' for <Reaction r_1101 at 0x111d9d4a8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER056C OR YER060W OR YER060W-A OR YGL186C)' for <Reaction r_1108 at 0x111d9da20>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBL030C OR YBR085W OR YMR056C)' for <Reaction r_1110 at 0x111d9dd30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR384C OR YGR121C OR YNL142W OR YPR138C)' for <Reaction r_1115 at 0x111da3390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER056C OR YER060W OR YER060W-A OR YGL186C)' for <Reaction r_1133 at 0x111da83c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL245C OR YDR342C OR YDR343C OR YDR345C OR YEL069C OR YFL011W OR YHR092C OR YHR094C OR YHR096C OR YJL214W OR YJL219W OR YJR158W OR YMR011W OR YNR072W OR YOL156W)' for <Reaction r_1134 at 0x111da85f8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR536W OR YFL011W OR YJL219W OR YLR081W OR YNL318C OR YOL156W)' for <Reaction r_1135 at 0x111da8cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL245C OR YDR342C OR YDR343C OR YDR345C OR YEL069C OR YFL011W OR YHR092C OR YHR094C OR YHR096C OR YJL214W OR YJL219W OR YJR158W OR YMR011W OR YNR072W OR YOL156W)' for <Reaction r_1139 at 0x111dae208>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1146 at 0x111dae940>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1147 at 0x111daea90>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1148 at 0x111daebe0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1161 at 0x111daee80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1162 at 0x111db6048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDL245C OR YDL247W OR YDR342C OR YDR343C OR YDR345C OR YDR536W OR YEL069C OR YFL011W OR YHR092C OR YHR094C OR YHR096C OR YJL214W OR YJL219W OR YJR158W OR YJR160C OR YLR081W OR YMR011W OR YNR072W OR YOL156W)' for <Reaction r_1166 at 0x111db62e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR135C OR YLL015W)' for <Reaction r_1168 at 0x111db6cc0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR536W OR YGL084C OR YPL189W)' for <Reaction r_1171 at 0x111dbb048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL025C OR YKR039W OR YOL020W OR YOR348C OR YPL265W)' for <Reaction r_1173 at 0x111dbb320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER056C OR YER060W OR YER060W-A OR YGL186C)' for <Reaction r_1176 at 0x111dbb748>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR497C OR YOL103W)' for <Reaction r_1177 at 0x111dbb978>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YCL025C OR YDR046C OR YKR039W OR YOL020W OR YOR348C OR YPL265W)' for <Reaction r_1183 at 0x111dbbd68>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL063C OR YKR039W OR YNL270C)' for <Reaction r_1184 at 0x111dc0160>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL025C OR YDR508C OR YKR039W OR YPL265W)' for <Reaction r_1186 at 0x111dc0400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL146W OR YNL101W)' for <Reaction r_1188 at 0x111dc0748>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YFL055W OR YKR039W OR YPL265W)' for <Reaction r_1190 at 0x111dc09b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YBR069C OR YCL025C OR YDR046C OR YDR508C OR YKR039W OR YOL020W)' for <Reaction r_1192 at 0x111dc0c88>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL025C OR YFL055W OR YKR039W OR YPL265W)' for <Reaction r_1196 at 0x111dc7320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL146W OR YNL101W)' for <Reaction r_1198 at 0x111dc7630>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL025C OR YDR508C OR YKR039W OR YPL265W)' for <Reaction r_1199 at 0x111dc77b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR293W OR YCL069W OR YMR088C)' for <Reaction r_1200 at 0x111dc79e8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR069C OR YGR191W OR YKR039W)' for <Reaction r_1201 at 0x111dc7ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL146W OR YNL101W)' for <Reaction r_1204 at 0x111dc7f28>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YBR069C OR YCL025C OR YDR046C OR YKR039W)' for <Reaction r_1205 at 0x111dcd0f0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL146W OR YNL101W)' for <Reaction r_1210 at 0x111dcd6d8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YBR069C OR YCL025C OR YDR046C OR YDR508C OR YKR039W)' for <Reaction r_1211 at 0x111dcd860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR293W OR YCL069W OR YMR088C)' for <Reaction r_1212 at 0x111dcdb70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKR039W OR YNL268W)' for <Reaction r_1213 at 0x111dcdd30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YCL025C OR YDR046C OR YDR508C OR YGR055W OR YHL036W OR YKR039W)' for <Reaction r_1214 at 0x111dcde80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YCL025C OR YDR046C OR YKR039W OR YOL020W)' for <Reaction r_1215 at 0x111dd3240>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKR039W OR YOR348C)' for <Reaction r_1216 at 0x111dd34e0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YCL025C OR YDR508C OR YFL055W OR YKR039W OR YPL265W)' for <Reaction r_1217 at 0x111dd3630>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR069C OR YCL025C OR YDR046C OR YDR508C OR YKR039W)' for <Reaction r_1218 at 0x111dd38d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YBR069C OR YDR046C OR YKR039W OR YOL020W)' for <Reaction r_1219 at 0x111dd3b70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR293W OR YJR001W)' for <Reaction r_1221 at 0x111dd3eb8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL146W OR YNL101W)' for <Reaction r_1222 at 0x111dd9080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YBR069C OR YCL025C OR YDR046C OR YKR039W OR YOL020W)' for <Reaction r_1223 at 0x111dd9208>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR068C OR YBR069C OR YCL025C OR YDR046C OR YKR039W)' for <Reaction r_1224 at 0x111dd9518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1225 at 0x111dd9780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR298C OR YDL247W OR YGR289C OR YJR160C)' for <Reaction r_1227 at 0x111dd99b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL006W OR YIL006W)' for <Reaction r_1229 at 0x111dd9cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YEL063C OR YKR039W)' for <Reaction r_1238 at 0x111ddd400>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR296C OR YCR037C OR YJL198W OR YML123C OR YNR013C)' for <Reaction r_1244 at 0x111ddd860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YER053C OR YJR077C)' for <Reaction r_1245 at 0x111dddb38>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLL028W OR YOR273C)' for <Reaction r_1251 at 0x111ddde80>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLL028W OR YOR273C)' for <Reaction r_1252 at 0x111de3048>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR132C OR YHL016C OR YKR039W OR YLL028W OR YOR273C OR YPL274W)' for <Reaction r_1260 at 0x111de3898>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLL028W OR YOR273C)' for <Reaction r_1261 at 0x111de3be0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR138C OR YLL028W OR YOR273C OR YPR156C)' for <Reaction r_1262 at 0x111de3d30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YGR138C OR YLL028W OR YOR273C OR YPR156C)' for <Reaction r_1263 at 0x111de3f60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YBR294W OR YLR092W)' for <Reaction r_1266 at 0x111de9390>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLR237W OR YOR071C OR YOR192C)' for <Reaction r_1270 at 0x111de9780>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YLL052C OR YPR192W)' for <Reaction r_1277 at 0x111de9f60>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YIL013C OR YOR011W)' for <Reaction r_1278 at 0x111def128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '((YGL080W AND YGR243W) OR (YGL080W AND YHR162W))' for <Reaction r_2034 at 0x111def2b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YOR222W OR YPL134C)' for <Reaction r_2132 at 0x111def588>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2219 at 0x111def710>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2220 at 0x111def860>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2221 at 0x111def9b0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2222 at 0x111defb00>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2223 at 0x111defc50>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2224 at 0x111defda0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2225 at 0x111defef0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2226 at 0x111df6080>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2227 at 0x111df61d0>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YKL188C AND YPL147W)' for <Reaction r_2228 at 0x111df6320>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3428 at 0x111e12b70>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3429 at 0x111e12cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3430 at 0x111e12e48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3431 at 0x111e12f98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3432 at 0x111e1a128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3433 at 0x111e1a278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3434 at 0x111e1a3c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3435 at 0x111e1a518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3436 at 0x111e1a668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3437 at 0x111e1a7b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3438 at 0x111e1a908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3439 at 0x111e1aa58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3440 at 0x111e1aba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3441 at 0x111e1acf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3442 at 0x111e1ae48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3443 at 0x111e1af98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3444 at 0x111e20128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3445 at 0x111e20278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3446 at 0x111e203c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3447 at 0x111e20518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3448 at 0x111e20668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3449 at 0x111e207b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3450 at 0x111e20908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3451 at 0x111e20a58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3452 at 0x111e20ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3453 at 0x111e20cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3454 at 0x111e20e48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3455 at 0x111e20f98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3456 at 0x111e28128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3457 at 0x111e28278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3458 at 0x111e283c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3459 at 0x111e28518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3460 at 0x111e28668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3461 at 0x111e287b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3462 at 0x111e28908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3463 at 0x111e28a58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3464 at 0x111e28ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3465 at 0x111e28d30>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3466 at 0x111e28e48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3467 at 0x111e28f98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3468 at 0x111e2f128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3469 at 0x111e2f278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3470 at 0x111e2f3c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3471 at 0x111e2f518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3472 at 0x111e2f668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3473 at 0x111e2f7b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3474 at 0x111e2f908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3475 at 0x111e2fa58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3476 at 0x111e2fba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3477 at 0x111e2fcf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3478 at 0x111e2fe48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3479 at 0x111e2ff98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3480 at 0x111e33128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3481 at 0x111e33278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3482 at 0x111e333c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3483 at 0x111e33518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3484 at 0x111e33668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3485 at 0x111e337b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3486 at 0x111e33908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3487 at 0x111e33a58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3488 at 0x111e33ba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3489 at 0x111e33cf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3490 at 0x111e33e48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3491 at 0x111e33f98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3492 at 0x111e3d128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3493 at 0x111e3d278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3494 at 0x111e3d3c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3495 at 0x111e3d518>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3496 at 0x111e3d668>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3497 at 0x111e3d7b8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3498 at 0x111e3d908>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3499 at 0x111e3da58>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3500 at 0x111e3dba8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3501 at 0x111e3dcf8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3502 at 0x111e3de48>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3503 at 0x111e3df98>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3504 at 0x111e42128>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3505 at 0x111e42278>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3506 at 0x111e423c8>
cobra/core/Reaction.py:96 UserWarning: malformed gene_reaction_rule '(YDR367W AND YKL004W)' for <Reaction r_3507 at 0x111e42518>

Constraints can be set in the model according to data found in the literature. The defined conditions allow the simulation of phenotypes very close to the experimental results.

**Model validation by comparing in silico prediction of the specific

growth rate with experimental data**. Growth phenotypes were collected from literature and compared to simulated values for chemostat cultivations at four different conditions, nitrogen limited aerobic (green) and anaerobic (red), carbon limited aerobic (blue) and anaerobic (white).

Österlund, T., Nookaew, I., Bordel, S., & Nielsen, J. (2013). Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Systems Biology, 7, 36. doi:10.1186/1752-0509-7-36

model.reactions.r_1714.lower_bound = -13 #glucose exchange
model.reactions.r_1992.lower_bound = -3  #oxygen exchange

model.medium

	reaction_id	reaction_name	lower_bound	upper_bound
0	r_1654	ammonium exchange	-1000	1000
1	r_1714	D-glucose exchange	-13	1000
2	r_1832	H+ exchange	-1000	1000
3	r_1861	iron(2+) exchange	-1000	1000
4	r_1992	oxygen exchange	-3	1000
5	r_2005	phosphate exchange	-1000	1000
6	r_2020	potassium exchange	-1000	1000
7	r_2049	sodium exchange	-1000	1000
8	r_2060	sulphate exchange	-1000	1000
9	r_2100	water exchange	-1000	1000

model.objective = model.reactions.r_2111 #growth
model.optimize().f

0.3925993816536346

Heterologous pathway

Vanillin is not produced by S. cervisiae. In their work an heterolgous pathway is inserted to allow generate a vanillin production strain. The pathway is described as:

**Schematic representation of the de novo VG biosynthetic pathway in S.

Cerevisisae** (as designed by Hansen et al [5]). Metabolites are shown in black, enzymes are shown in black and in italic, cofactors and additional precursors are shown in red. Reactions catalyzed by heterologously introduced enzymes are shown in red. Reactions converting glucose to aromatic amino acids are represented by dashed black arrows. Metabolite secretion is represented by solid black arrows where relative thickness corresponds to relative extracellular accumulation. 3-DSH stands for 3-dedhydroshikimate, PAC stands for protocathechuic acid, PAL stands for protocatechuic aldehyde, SAM stands for S-adenosylmethionine. 3DSD stands for 3-dedhydroshikimate dehydratase, ACAR stands for aryl carboxylic acid reductase, PPTase stands for phosphopantetheine transferase, hsOMT stands for O-methyltransferase, and UGT stands for UDP-glycosyltransferase. Adapted from Hansen et al. [5]. Brochado et al. Microbial Cell Factories 2010 9:84 doi:10.1186/1475-2859-9-84

Using cameo, is very easy to generate a pathway and add it to a model.

from cameo.core.pathway import Pathway

vanillin_pathway = Pathway.from_file("data/vanillin_pathway.tsv")
vanillin_pathway.data_frame

	equation	lower_bound	upper_bound
3DSD	3-dehydroshikimate --> protocathechuic acid + H2O	0	1000
ACAR_PPTase	ATP + protocathechuic acid + NADPH --> ADP + N...	0	1000
hsOMT	protocatechuic aldehyde + S-adenosyl-L-methion...	0	1000
UGT	UDP-glucose + Vanillin --> vanillin-B-glucoside	0	1000

And now we can plug the pathway to the model.

vanillin_pathway.plug_model(model)

from cameo import phenotypic_phase_plane

production_envelope = phenotypic_phase_plane(model, variables=[model.reactions.r_2111],
                                             objective=model.reactions.EX_vnlBglu)
production_envelope.plot()

To find gene knockout targets, we use cameo.strain_design.heuristic package which implements the OptGene strategy.

The authors used the biomass-product coupled yield (bpcy) for optimization which is the equivalent of running OptGene in non-robust mode. All simulations were computed using MOMA but because cameo does not implement MOMA we use it’s equivalent linear version (it minimizes the absolute distance instead of the quadratic distance). The linear MOMA version is faster than the original MOMA formulation.

from cameo.strain_design.heuristic.evolutionary_based import OptGene
from cameo.flux_analysis.simulation import lmoma

optgene = OptGene(model)

%prun optgene.run(target="EX_vnlBglu", biomass="r_2111", substrate="r_1714", simulation_method=lmoma, robust=False)

INFO:cameo.strain_design.heuristic.evolutionary.optimization:No WT reference found, generating using pfba.

Starting optimization at Thu, 14 Jan 2016 15:30:20

Using saved session configuration for http://localhost:5006/
To override, pass 'load_from_config=False' to Session

/Users/joao/.virtualenvs/cameo-py3/lib/python3.4/site-packages/bokeh/session.py:318 UserWarning: You need to start the bokeh-server to see this example.

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